vacalibration (version 2.0)

comsamoz_public_openVAout: COMSA-Mozambique: Example Individual-Level Specific (High-Resolution) Cause of Death Data (Publicly Available Version)

Description

Example individual‑level neonatal cause‑of‑death data using InSilicoVA. This is obtained by applying InSilicoVA algorithm and crossVA mapping in the openVA package. This provides specific (high-resolution) cause of death for each individual.

Usage

comsamoz_public_openVAout

Format

A list of 4 components.

data

Data frame. Contains the data. Rows are individuals. It has 2 columns. First column "ID" is the individual ID. Second column "cause" are the high-resolution causes of deaths.

age_group

Character. Indicate age group. "neonate" (for 0-27 days) for this data

va_algo

Character. Indicate CCVA algorithm. "insilicova" for this data

version

Character. Date stamp for version control of tracking updates. Only for package maintainers.

Details

comsamoz_public_openVAout$data$ID[i] is the ID for individual i.

comsamoz_public_openVAout$data$cause[i] is the specific cause of death for individual i.

References

Macicame, I, et al. (2023). Countrywide Mortality Surveillance for Action in Mozambique: Results from a National Sample-Based Vital Statistics System for Mortality and Cause of Death. American Journal of Tropical Medicine and Hygiene, 108(Suppl 5), pp. 5–16.

Examples

# \donttest{

## using the data (as output by crossVA function in openVA package for InSilicoVA algorithm)
data(comsamoz_public_openVAout)
head(comsamoz_public_openVAout$data)  # head of the data
comsamoz_public_openVAout$data[1,]  # ID and specific cause of death for individual 1

## mapped to broad cause
### same as comsamoz_public_broad$data
comsamoz_public_asbroad = cause_map(df = comsamoz_public_openVAout$data, age_group = "neonate")
head(comsamoz_public_asbroad)

### store broad cause map of the data
data(comsamoz_public_broad)
head(comsamoz_public_broad$data) # identical to head(comsamoz_public_asbroad)

## mapped to national death counts
comsamoz_public_asdeathcount = colSums(comsamoz_public_asbroad)

## VA-calibration for the "neonate" age group and InSilicoVA algorithm
## input as specific cause
calib_out_asspecific = vacalibration(va_data = setNames(list(comsamoz_public_openVAout$data),
                                                     list(comsamoz_public_openVAout$va_algo)),
                                     age_group = comsamoz_public_openVAout$age_group,
                                     country = "Mozambique")

## input as broad cause
calib_out_asbroad = vacalibration(va_data = setNames(list(comsamoz_public_asbroad),
                                                     list(comsamoz_public_openVAout$va_algo)),
                                     age_group = comsamoz_public_openVAout$age_group,
                                     country = "Mozambique")

## input as specific cause
calib_out_asdeathcount = vacalibration(va_data = setNames(list(comsamoz_public_asdeathcount),
                                                          list(comsamoz_public_openVAout$va_algo)),
                                       age_group = comsamoz_public_openVAout$age_group,
                                       country = "Mozambique")

## comparing uncalibrated CSMF estimates and posterior summary of calibrated CSMF estimates
calib_out_asspecific$p_uncalib
calib_out_asspecific$pcalib_postsumm[1,,]

calib_out_asbroad$p_uncalib
calib_out_asbroad$pcalib_postsumm[1,,]

calib_out_asdeathcount$p_uncalib
calib_out_asdeathcount$pcalib_postsumm[1,,]

# }